installing qiime with docker

I was running qiime with virtual box successfully, all of the sudden i can not use the classifier due to sklearn issue, i checked the forum and saw similar issue suggesting updating the version. very unfortunately i cannot see virtual box again which makes make back to square zero. I tried installing with docker this happened. it is really frustrating

Hi @Zango,

I think the issue is you are using a BASH trick inside of Powershell, which won't understand $(pwd). Instead you I think that this volume argument is what you want:

-v "$pwd:/data"

Powershell still has the alias for pwd to Get-Location but probably doesn't care to understand what the sub-shell invocation means $(<some command>) so I think that's why you are getting that issue.

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Thank you for the reply, I installed it with the command, however before i was using a virtualbox shared folder for my analysis but now in docker, a very big problem is how can i share my folder with docker to run the analysis?
Thank you once again

Hi @Zango,

That is precisely what the -v option does. It mounts a docker volume.

Out of curiosity, do you have Windows Subsystem for Linux available on your machine? If so, that will be significantly simpler than either docker or VirtualBox ever was. Your C:\ drive is automatically mounted and it's otherwise a normal linux terminal (but inside Windows).

Thank you @ebolyen for your helpful guidance, my machine has Windows Subsystem for Linux enabled on, and i already downloaded Debian. How can i precede. Thanks for the reply and stay blessed

Perfect, launch the Debian program from your start menu and it should open a linux terminal. From there you can install miniconda and use our linux environment file (or the WSL one, which is identical) to install QIIME 2.

To access your files, they are automatically available within /mnt/c/ (you probably want to specify the rest of your path, but that will be the regular C drive, do mind the difference between windows paths which are separated by \
-- While in the linux subsystem, they will all become / instead).

Importantly, you will also have a regular linux filesystem. I believe there is technically a way to access files inside the linux end from the windows end, but I would suggest either doing your work in /mnt/c/Users/<you>/<whatever> or copying things into and out of that directory as you desire.

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Thank you @ebolyen i followed your suggestions, but i encountered another problem during installation of qiime, and i could not find the solution of my problem in the forum so created a new topic on that. Thank you

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